hey.....
i do have text where the contents are like as follows,
FILE_TYPE_NUM_01=FILE_TYPE=01|FILE_DESC=Periodic|FILE_SCHDL_TYPE=Daily|FILE_SCHDL=|FILE_SCHDL_TIME=9:00am|RESULTS=B
FILE_TYPE_NUM_02=FILE_TYPE=02|FILE_DESC=NCTO|FILE_SCHDL_TYPE=Daily|FILE_SCHDL=|FILE_SCHDL_TIME=9:00am|RESULTS=M... (2 Replies)
Hi,
I have an array with 3 words in it and i have to match all the array contents and display the exact matched sentence i.e all 3 words should match with the sentence.
Here are sentences.
$arr1="Our data suggests that epithelial shape and growth control are unequally affected depending... (5 Replies)
Hi
By using select clause I'm trying to pull out the rows to a variable.
If the variable has 0 row(s) selected then i'm printing some text message
else printing some other text message
if($xyz =~ m/0 row/)
{
print "0 rows ";
}
else
{
print " There are rows";
}
By my problem... (4 Replies)
I am trying to match a pattern exactly in a shell script. I have tried two methods
awk '/\<mpath${CURR_MP}\>/{print $1 $2}' multipath
perl -ne '/\bmpath${CURR_MP}\b/ and print' /var/tmp/multipath
Both these methods require that I use the escape character. I am guessing that is why... (8 Replies)
Hi,
I have a file like follows
.
.
.
White.Jack.is.going.home
Black.Jack.is.going.home
Red.Jack.is.going.home
Jack.is.going.home
.
.
.
when I make:
cat <file> | grep -w "Jack.is.going.home"
it gives:
White.Jack.is.going.home
Black.Jack.is.going.home
Red.Jack.is.going.home... (4 Replies)
Hi friends,
i am using the following grep command for exact word match:
>echo "sachin#tendulkar" | grep -iw "sachin"
output: sachin#tendulkar
as we can see in the above example that its throwinng the exact match(which is not the case as the keyword is sachin and string is... (6 Replies)
Dear all, could you help me with following question. There are two datasets (below). I need to find match between BP values from data1 and data2, and add corresponding CM value from data2 into data1. if there is not exact match, the corresponding CM value should be calculated using interpolation.... (20 Replies)
Hi All,
I am breaking my head in trying to get a command that will exactly match my given string. I have searched net and found few of the options -
grep -F $string file
grep -x $string file
grep "^${string}$" file
awk '/"${string}"/ {print $0}' file
strangely nothing seems to... (3 Replies)
Hello!
I have 2 files named tacs.tmp and tacDB.txt
tacs.tmp looks like this
0
10235647
102700
106800
107200
1105700
tacDB.txt looks like this
100100,Mitsubishi,G410,Handheld,,0,0,0
100200,Siemens,A53,Handheld,,0,0,0
100300,Sony Ericsson,TBD (AAB-1880030-BV),Handheld,,0,0,0... (2 Replies)
I am trying to create a cronjob that will run on startup that will look at a list.txt file to see if there is a later version of a database using database.txt as the source. The matching lines are written to output.
$1 in database.txt will be in list.txt as a partial match. $2 of database.txt... (2 Replies)
Discussion started by: cmccabe
2 Replies
LEARN ABOUT DEBIAN
theseus_align
THESEUS_ALIGN(1) General Commands Manual THESEUS_ALIGN(1)NAME
theseus_align - quick-and-dirty way to superimpose proteins
SYNOPSIS
theseus_align [theseus options] -f pdbfile1.pdb pdbfile2.pdb ...
OPTIONS
The options given to the script will be passed on to theseus. For a complete description, see the man page for theseus (1).
DESCRIPTION
This manual page briefly documents briefly the script theseus_align, designed for a quick-and-dirty way to ML superposition proteins with
different sequences. It should work very well when the protein sequences are relatively similar, although the ML method will still give
much better results than least-squares when the sequences are moderately divergent. Technically, this procedure gives a structure-based
superposition of a sequence-based alignment. It does not perform a structure-based alignment.
First, the script uses theseus to create FASTA formatted sequence files corresponding to the exact protein sequences found in the pdb files
that you supply.
Second, these sequences are aligned using the multiple sequence alignment program of your choice. The script can easily be modified for
CLUSTALW, T_COFFEE, KALIGN, DIALIGN2, or MAFFT. Any multiple sequence alignment program can be used, as long as it can generate clustal-
formatted files. However, I highly recommend Bob Edgar's MUSCLE program for both its speed and accuracy. (For more info see
http://www.drive5.com/muscle/ .)
Third, theseus performs a superposition of the structures using the sequence alignment as a guide.
The installed version of theseus_align uses muscle (1) for doing the multiple sequence alignment. If you wish to use one of the other pro-
grams mentioned above, you'll have to copy the script to your own directory and edit it.
SEE ALSO
theseus (1), muscle (1), clustalw (1), t_coffee (1), kalign (1), dialign2 (1), mafft (1). All of these programs can be installed on Debian
or Ubuntu systems using apt-get (8).
AUTHOR
theseus_align was written by Douglas L. Theobald, Department of Biochemistry, Brandeis University.
November, 2008 THESEUS_ALIGN(1)